https://github.com/bcgsc/pori

Platform for Oncogenomic Reporting and Interpretation (PORI)
https://github.com/bcgsc/pori

genomics personalized-medicine pori

Last synced: 7 days ago
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Platform for Oncogenomic Reporting and Interpretation (PORI)

• Host: GitHub
• URL: https://github.com/bcgsc/pori
• Owner: bcgsc
• License: gpl-3.0
• Created: 2021-01-07T18:24:47.000Z (almost 4 years ago)
• Default Branch: master
• Last Pushed: 2024-07-04T19:27:37.000Z (4 months ago)
• Last Synced: 2024-10-13T14:15:29.888Z (about 1 month ago)
• Topics: genomics, personalized-medicine, pori
• Language: Shell
• Homepage: https://bcgsc.github.io/pori
• Size: 12.9 MB
• Stars: 30
• Watchers: 7
• Forks: 6
• Open Issues: 8
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Platform for Oncogenomic Reporting and Interpretation (PORI)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5728140.svg)](https://doi.org/10.5281/zenodo.5728140)

The Platform for Oncogenomic Reporting and Interpretation (PORI) is an open source collection of

software designed to support scaleable precision oncology. The platform has two main components:

a graph knowledge base (GraphKB) and an integrated pipeline reporting application (IPR).

![pori server stack](./docs/images/pori-server-stack.png)

For more information see the related [user manual](https://bcgsc.github.io/pori)

## Demo

A live demo of this is found at: [pori-demo.bcgsc.ca](https://pori-demo.bcgsc.ca). This demo was

deployed via docker-compose

## Citation

Please cite [Reisle, C. et al. A platform for oncogenomic reporting and interpretation. Nat. Commun. 13, 1–11 (2022)](https://www.nature.com/articles/s41467-022-28348-y)

## Building the Docs (Developers)

The main PORI site is built from this repo and pull documentation files from the python adapter repos. The documentation is built using mkdocs. The main website

will be updated on merge to the master branch of this repository.

First, set up a virtual environment (Optional but recommended)

```bash

python3 -m venv venv

source venv/bin/activate

pip install -U setuptools pip

```

Install the python dependencies

```bash

pip install -r requirements.txt

```

Run the script to pull the other respository files

```bash

bash docs/build_external.sh

```

And finally serve the documentation for viewing locally with

```bash

mkdocs serve

```